5b85

X-ray structure of ferric F138Y sperm whale myoglobin

Method: X-RAY DIFFRACTION Dmax: 50.6 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Myoglobin

Physeter catodon

UniProt P02185

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 2–154 Fragment:UNP residues 2-154 Mutation:F138Y HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;30%(w/v) Polyethylene glycol 8,000, 0.1M Sodium cacodylate trihydrate pH 6.5, 0.2M Sodium acetate trihydrate Resolution 1.85 Å R-free 0.224

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

354 other PDB entries and 366 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYG_PHYCD
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–153; UniProt 2–154

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5b85

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5b85
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5b85
Deposition date deposition_date2016-06-12
Structure title titleX-ray structure of ferric F138Y sperm whale myoglobin
Keywords keywordsoxygen storage; OXYGEN STORAGE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.47
Radius of gyration Rg (electron density) rg_electron15.05
Forward intensity I(0) i05597650.00
Molecular weight molecular_weight17773.0 kDa
Excluded volume excluded_volume22538 ų
Envelope volume envelope_volume24686 ų
Hydration-shell volume shell_volume13895 ų
Envelope diameter envelope_diameter51.7
Shell Rg shell_rg20.92
Envelope Rg envelope_rg15.26
Shape Rg shape_rg15.04
Total Rg total_rg16.22
Total atoms total_atoms1257
Residues n_residues153
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.6
Rg (real space) rg_real16.35
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real5.5980e+06
I(0) uncertainty (real space) i0_real_error6.7700e+04
Rg (reciprocal space) rg_reciprocal16.36
I(0) (reciprocal space) i0_reciprocal5598000.0000
Solution quality estimate total_estimate0.8235
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.9
Skewness Skewness skewness0.091
Kurtosis Kurtosis kurtosis-0.457
Angular range angular_range— – 0.4850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha844700.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5b85a_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins

CATH v4.4 (1 domains)

Domain ID domain_id5b85A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins

8. Citations (1)

9. Files and Curves (10)